Showed a distinct behavior of the ATP lid between PaNTD and

Showed a distinct behavior of the ATP lid between PaNTD and EcNTD. Snapshots of the conformation sampled by the ATP lid (residues 747 for EcNTD and 7801 for PaNTD) along the trajectories are shown in Figure 3. Figure S2 shows the secondary structure of the full dimerization interface as a function of time. Apo EcNTD ATP lid undergoes a significant structural change early in the simulation. The helix between residues 818 is lost and not recovered for the rest of the simulation (Figure 3 and Figure S2). On the other hand, in the holo form of EcNTD as well in both forms of PaNTD, the ATP lid maintains its a-helical structure along the whole MD trajectory (Figure 3 and Figure S1). Ban Yang experimental results [15] show that in EcNTD crystal structure, ATP lid becomes more mobile in ADP-bound and nucleotide free forms in comparison to ATP-bound, but remains partially structured. Although EcNTD DP crystal structure is dimeric, probably due to crystal packing, this complex is a monomer in solution. Also, inthe absence of the c-phosphate, ATP lid becomes more mobile as indicated by higher B values [15]. An analysis of PaNTD and EcNTD ATP lid alignment shows that ATP lid helix is conserved (Figure 1). Nevertheless when the highly reliable and experimentally calibrated AGADIR prediction algorithm [41] was used to calculate the a-helix propensity of these two isolated regions, the alpha helix propensity was larger for the PaNTD sequence than for the EcNTD (Figure S3). This result is in line with MD simulations.Structure Based Molecular Dynamics Simulations in Presence or in Absence of Adenine Nucleotides Reflect a Differential Behavior of PaNTD and EcNTD Dimerization InterfaceBased on the funneled nature of the energy landscape of protein folding [42], structure based models (SBM) provide a computationally efficient and reliable model to explore the large scale molecular motions of proteins which are no reachable with more detailed models as used in the previous section.Aspirin MD simulations of SBM were performed to further analyze the difference between proteins under study.Tegafur-Uracil These simulations were run for a time long enough to guarantee that the root mean squared fluctuations (RMSF) calculated with one half of the trajectory is identical to the calculated with the second half.PMID:23514335 This kind of converged picture is not possible to achieve with the 200 ns of simulations that were performed with the most complete model used in the previous section, and it is of fundamental importance as we seek for the difference between two of such RMSF curves. Figure 4A shows the difference in RMSF (D RMSF) between the apo and ATP bound forms of each protein (full line: PaNTD; dotted line: EcNTD). It is observed that the apo forms showed a more flexible structure for both species. This result is in line with the reduction in secondary structure observed for apo proteins during the explicit solvent MD simulations (Figure S1B). More importantly for this work, this analysis clearly revealed the presence of 5 regions with different behavior between EcNTD and PaNTD. Residues corresponding to the dimerization interface, namely loops L1, L2, L3, L45 and the ATP lid were more mobile in apo EcNTD than in apo PaNTD. Also, the difference in RMSF between the ADP and ATP bound forms was calculated (Figure 4B). When DRMSF for ADP and ATP-Bound EcNTD was calculated (Figure 4A, full line), it was clear that the ADP bound showed higher mobility of the dimerization interface. This is refl.